Tripal User's Meeting 2021/04/06

Meeting Date
Attendees

Douglas Senalik, UW Madison + USDA ARS VCRU (CarrotOmics)
Risharde Ramnath, TreeGenes (UCONN) + WSU
Monica Poelchau, USDA NAL (i5k workspace)
Stephen Ficklin, Katheryn Buble, Sook Jung, Taein Lee, Chun-Huai Cheng WSU
Noah Caldwell, UTK
Irene Cobo, CartograTree/Plant (UConn)
Sean Buehler, i5k, UTK
Lilia Mesina, AAFC, Canada (Bee Portal)

Agenda

  1. Notices for the Advisory Committee
  2. An introduction to the Main Lab Breeding Module by Taein Lee
    • Breeding Information Management System
    • BIMS Overview
      • secure and comprehensive online breeding data management system.
      • store, manage, backup private breeding data.
      • comparable with the field back app (an android app for collecting data in the field)
      • BIMs is installed on all Main Lab databases, including GDR under the Tools menu.
      • Online documentation at https://www.breedwithbims.org/ 
      • You can access public data and there are private data only accessible to breeders.
      • Mange Breeding
        1. Manage Program
          1. Can add users
        2. Manage Traits
          1. Can manage all traits used by the program 
          2. Can view plots of usage of each trait
        3. Accessions
          1. You can view details about each accession (organism and parental information).  
        4. Trials
          1. You can view information about trials
      • Data Import
        1. Can import data using the BIMS t template file. There are various templates for different data types, or you can download a single template of all.
        2. Templates are excel files with headers.  Users can add data to the template files and use those to import data into BIMS.
      • Field Book Management Page
        1. On this page you can import data from the field book.
        2. Export field file from the field book app and import it on this page.
      • Archive page
        1. Allows you to retrieve previously uploaded data files.
        2. Can create new archive files for download so you have a backup of data in BIMS
      • Search
        1. You can search for phenoyptes, crosses, genotypes (SNP/SSR), Haplotypes. 
        2. Search results show histogram of selected trait.  
        3. Search results page has a default set of columns but you can add any column of interest to expand the results table.  
      • BIMS is currently available at https://gitlab.com/mainlabwsu/bims
      • It is a Drupal 7 module.  
      • Limitations
        1. Does not currently handle the organism table of Chado v1.3 (due to addition of infraspecific name).  
        2. Uses BrAPI 1.3 but currently BrAPI is at 2.0
      • Requirements
        1. Mainlab Chado Loader
        2. OAuth 2 SErver
        3. Breeding API module
          1. Druplal 7, BrAPI 1.3
Meeting Type
Users